Performs t-SNE reduction

Performs t-SNE reduction on defined method-assays and supplied reductions or graphs.

perform.tsne(
  object,
  assay,
  reduction = NULL,
  reduction.name.suffix = "",
  n.dims = NULL,
  n_components = 3,
  ...
)

Arguments

object

IBRAP S4 class object

assay

Character. String containing indicating which assay to use

reduction

Character. String defining which reduction to supply to the t-SNE algorithm. Default = NULL

reduction.name.suffix

Character. What should be appended to the end of tsne as the reduction name.

n.dims

Numerical. How many dimensions of the supplied reduction be used, Null equates to all dimensions. Default = NULL

n_components

Numerical. How many tsne dimensions should be produced, if you are supplying graphs, only 2 dimensions can be produced. Default = 3

...

Numerical. Arguments to be passed to ProjectionBasedClustering::tSNE

Value

UMAP reduction saved in the visualisation_reductions section in the supplied method-assays